diff options
| -rw-r--r-- | gn3/db/sample_data.py | 33 |
1 files changed, 17 insertions, 16 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py index f4ce64a..446d18d 100644 --- a/gn3/db/sample_data.py +++ b/gn3/db/sample_data.py @@ -610,6 +610,7 @@ def insert_sample_data( def batch_update_sample_data( conn: Any, diff_data: Dict ): + """Given sample data diffs, execute all relevant update/insert/delete queries""" def __fetch_data_id(conn, db_type, trait_id, dataset_name): with conn.cursor() as cursor: if db_type == "Publish": @@ -635,7 +636,7 @@ def batch_update_sample_data( ) return cursor.fetchone()[0] - def __fetch_strain_id(cursor, strain_name): + def __fetch_strain_id(conn, strain_name): with conn.cursor() as cursor: cursor.execute( "SELECT Id FROM Strain WHERE Name = %s", (strain_name,) @@ -648,24 +649,24 @@ def batch_update_sample_data( cursor.execute( ( f"UPDATE {db_type}Data " - f"SET value = %s " - f"WHERE Id = %s AND StrainId = %s" + "SET value = %s " + "WHERE Id = %s AND StrainId = %s" ), (diffs['value']['Current'], data_id, strain_id) ) if 'error' in diffs: cursor.execute( ( f"UPDATE {db_type}SE " - f"SET error = %s " - f"WHERE DataId = %s AND StrainId = %s" + "SET error = %s " + "WHERE DataId = %s AND StrainId = %s" ), (diffs['error']['Current'], data_id, strain_id) ) if 'n_cases' in diffs: cursor.execute( ( - f"UPDATE NStrain " - f"SET count = %s " - f"WHERE DataId = %s AND StrainId = %s" + "UPDATE NStrain " + "SET count = %s " + "WHERE DataId = %s AND StrainId = %s" ), (diffs['n_cases']['Current'], data_id, strain_id) ) @@ -677,21 +678,21 @@ def batch_update_sample_data( cursor.execute( ( f"INSERT INTO {db_type}Data (Id, StrainId, value)" - f"VALUES (%s, %s, %s)" + "VALUES (%s, %s, %s)" ), (data_id, strain_id, diffs['value']) ) if 'error' in diffs: cursor.execute( ( f"INSERT INTO {db_type}SE (DataId, StrainId, error)" - f"VALUES (%s, %s, %s)" + "VALUES (%s, %s, %s)" ), (data_id, strain_id, diffs['error']) ) if 'n_cases' in diffs: cursor.execute( ( - f"INSERT INTO NStrain (DataId, StrainId, count)" - f"VALUES (%s, %s, %s)" + "INSERT INTO NStrain (DataId, StrainId, count)" + "VALUES (%s, %s, %s)" ), (data_id, strain_id, diffs['n_cases']) ) @@ -703,21 +704,21 @@ def batch_update_sample_data( cursor.execute( ( f"DELETE FROM {db_type}Data " - f"WHERE Id = %s AND StrainId = %s" + "WHERE Id = %s AND StrainId = %s" ), (data_id, strain_id) ) if 'error' in diffs: cursor.execute( ( f"DELETE FROM {db_type}SE " - f"WHERE DataId = %s AND StrainId = %s" + "WHERE DataId = %s AND StrainId = %s" ), (data_id, strain_id) ) if 'n_cases' in diffs: cursor.execute( ( - f"DELETE FROM NStrain " - f"WHERE DataId = %s AND StrainId = %s" + "DELETE FROM NStrain " + "WHERE DataId = %s AND StrainId = %s" ), (data_id, strain_id) ) |